REDCAT Documentation Table of Contents
- Download and Installation instructions
- File Formats
- Monte Carlo Sampling
- Main Gui
- Viewing and Interpreting Results
- Menu Items
The REDCAT File Format
Input to REDCAT consists of nine space delimited columns of data for every RDC entry. The nine columns are: x, y and z coordinates of the first atom, x, y and z coordinates of the second atom, experimental RDC, maximum RDC for that vector type at 1 A distance and measurement error. You can refer to “1a1z.redcat” that is included with this package as an example. The following is an example input line:
-7.679 10.035 5.255 -6.713 10.289 5.296 14.789 24350 1 /*from 2*/
Note that any information after the 9th column is considered to be comment. For backward compatibility, you may choose to start and end the comment section with /* and */ (just like commenting in C). The input file can either be prepared manually or using the "Prepare Input" function of REDCAT.
In preparing your input file please ensure that the following criteria are met:
- There should be no leading or trailing spaces in the input files.
- Each datum in the input file needs to be separated by only one delimiter. Do not put multiple spaces or tabs in the input file to make it esthetically pleasing to the eye.
- No datum should be left out, for missing data, include 999 (discussed below).
- There should be no blank lines at the beginning, in the middle or at the end of the input file.
The following values of RDC have special meaning and are reserved for specific use:
- A RDC value of 999 is interpreted as a missing value and will automatically be excluded from all analyses.
- A RDC value of “AVG” will indicate an averaging of the RDC values. For more information on this option please refer to Tutorial 4.
REDCAT State File
The REDCAT State file
The Dynamic Averaging File Format
The Dynamic Averaging file consist of one line per molecular state with three sections per line: the type of rotation used, data describing the rotation, and the percentage of time that the molecule is in the described conformation. There are two types of rotations specified:
- Rotation about a specified axis and a specified vector
- Z-Y-Z Euler Rotation given &alpha, &beta, and &gamma
If the rotation is to be done by defining an axis, a 0 is placed in the first column. Next, the x, y, and z coordinate describing the vector of the axis is specified in the second, third, and fourth column, respectively. The fifth column is the angle in degrees to rotate about the defined rotation axis, and the sixth column is the percent of time the domain is in this conformation.
0 1 2 3 0 0.33334 0 1 2 3 120 0.33333 0 1 2 3 240 0.33333
If the rotation is done by Z-Y-Z Euler Rotation, a 1 is placed in the first column. Next the &alpha, &beta, and &gamma values are placed in the second, third, and fourth column, respectively. The fifth column is the percentage of time the domain is in this conformation.
1 -3.10382 170.129 -72.0006 0.33333 1 -3.10382 170.129 -72.0006 0.33333 1 -3.10382 170.129 -72.0006 0.33333
The two rotation formats can also be combined within a single file. Whitespace between values is not an issue, so using tabs or any number of spaces between values will still yield the same result. For more information on Dynamic Averaging, please refer to Tutorial 3 as well as the Main Gui section of this site.
The Ensemble Solutions File Format
The Ensemble Solutions File is a single column list of REDCAT file locations. Each file location must be specified statically, that is, the full path to the REDCAT file should be specified.
As an example:
/opt/Redcat/data/1a1z.M1.redcat /opt/Redcat/data/1a1z.M2.redcat /opt/Redcat/data/1a1z.M3.redcat
Here the three REDCAT files are the same structure each with a separate alignment medium. For more information, please refer to the Main Gui section of this site.